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Book Sections Year : 2012

Roadmap for annotating transposable elements in eukaryote genomes

Timothée T. Flutre
Hadi H. Quesneville

Abstract

Current high-throughput techniques have made it feasible to sequence even the genomes of non-model organisms. However, the annotation process now represents a bottleneck to genome analysis, especially when dealing with transposable elements (TE). Combined approaches, using both de novo and knowledge-based methods to detect TEs, are likely to produce reasonably comprehensive and sensitive results. This chapter provides a roadmap for researchers involved in genome projects to address this issue. At each step of the TE annotation process, from the identification of TE families to the annotation of TE copies, we outline the tools and good practices to be used
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hal-00956367 , version 1 (06-03-2014)

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Emmanuelle E. Permal, Timothée T. Flutre, Hadi H. Quesneville. Roadmap for annotating transposable elements in eukaryote genomes. Mobile Genetic Elements, 859 (2 ed.), Springer Science + Business Media LLC, 308 p., 2012, Methods in molecular biology (Clifton, N.J.), 978-1-61779-602-9. ⟨10.1007/978-1-61779-603-6_3⟩. ⟨hal-00956367⟩

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